Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics
Nucleic Acids Research
Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics
Jyotsana J. Parmar 1
Dibyendu Das 0
Ranjith Padinhateeri 1
0 Department of Physics, Indian Institute of Technology Bombay , Mumbai 400076 , India
1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai 400076 , India
It is being increasingly realized that nucleosome organization on DNA crucially regulates DNA-protein interactions and the resulting gene expression. While the spatial character of the nucleosome positioning on DNA has been experimentally and theoretically studied extensively, the temporal character is poorly understood. Accounting for ATPase activity and DNA-sequence effects on nucleosome kinetics, we develop a theoretical method to estimate the time of continuous exposure of binding sites of nonhistone proteins (e.g. transcription factors and TATA binding proteins) along any genome. Applying the method to Saccharomyces cerevisiae, we show that the exposure timescales are determined by cooperative dynamics of multiple nucleosomes, and their behavior is often different from expectations based on static nucleosome occupancy. Examining exposure times in the promoters of GAL1 and PHO5, we show that our theoretical predictions are consistent with known experiments. We apply our method genomewide and discover huge gene-to-gene variability of mean exposure times of TATA boxes and patches adjacent to TSS (+1 nucleosome region); the resulting timescale distributions have non-exponential tails.
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One of the crucial contributor to cellular function and fate
is the ‘state’ of its chromatin, which is a dynamic
structure formed of DNA and myriads of proteins (1–3). The
key constituents of the chromatin are nucleosomes––DNA
wrapped around histone octamer (4). It is thought that one
major role of nucleosomes is to occlude certain DNA
sequences from getting exposed and thereby prevent
uncontrolled binding of non-histone proteins at various crucial
locations (5). However, during important cellular processes
(e.g. transcription, replication and DNA-repair),
nucleosome disassembly paves the way for local DNA accessibility
(6,7). Once these processes are completed, the DNA
typically wraps back and reassembles into nucleosomes (8). This
constant wrapping, unwrapping and relocation of
nucleosomes are assisted by ATP-dependent chromatin
remodelers (e.g. RSC, SWI/SNF, ACF) (9–12). Thus the interplay
of nucleosome dynamics and binding of non-histone
proteins regulate the ‘state’ of chromatin and its corresponding
functionality.
A major focus of many recent experiments has been to
understand the nature of positioning of nucleosomes along
DNA and the factors that control this positioning. This is
achieved by measuring a physical quantity known as
nucleosome occupancy (8,13–18). It is the probability of coverage
of a base pair (bp) of DNA by a nucleosome, obtained from
an ensemble of cells under same conditions, using MNase
digestion, chemical cleavage, etc. (13–15,18,19). Such
studies over years have shown that the in vivo positioning is
influenced by a number of factors such as ATP-dependent
molecular machines (11,13), DNA sequence (15,20–22) and
‘barriers’ that create nucleosome free region (NFR) near
transcription start site (TSS) (13,23,24). Even though the
occupancy gives us an idea about the spatial heterogeneity
of occluded regions along DNA, the quantity results from
superposition of several frozen snapshots. Hence, it cannot
give us information about the temporal variability of the
occluded regions and accessibility of DNA, which is crucial
for many cellular processes like gene regulation.
It is known that gene regulation, transcription, etc. are
kinetically driven processes with many non-histone proteins
(transcription factors (TFs), TATA-binding protein (TBP)
and RNA polymerase (RNAp) complex) binding on to the
DNA competing with the nucleosomes. One crucial
factor that controls the binding of these proteins is the
availability of continuously exposed (empty, having no proteins
bound) patches of DNA. The kinetics of nucleosomes play
an important role in regulating this continuous exposure
(25–27). For example, disassembly of nucleosomes is known
to be important for exposure of TATA sites in promoters
(19,28,29), while dynamics of +1 nucleosome is likely to
influence the accessibility near TSS (30). Sliding of
nucleosomes (31,32) as well as partial unwrapping/wrapping (33)
of DNA at nucleosome edges may also contribute toward
creating exposed regions along DNA. All such kinetic
activities, which are stochastic, can collectively influence
transcription levels and noise in gene expression.
In this context, it is important to stress the difference
between the study of temporal versus static positioning
(occupancy) of nucleosomes. As shown in Figure 1(A and B),
nucleosome with two sets of kinetic rates: (i) k+ = k− = 0.1s−1
or (ii) k+ = (...truncated)